opencobra/cobrapy — pull request #57 by aebrahim (2014-01-09 23:06:17+00:00)
Title: ArrayBasedModel has updateable arrays and matrix

The general idea is that doing the following actions propagates to the cobrapy objects

```python
model.S[1, 1] = 2
model.lower_bounds[4] = -1000
model.objective_coefficient = zeros(len(model.reactions))
model.objective_coefficient[10] = 1
```

A few things need to be done before this feature is completed.

* [x] S Matrix updating changes stoichiometry (through SMatrix class)
* [ ] SMatrix class for all sparse types, handling conversion (i.e. SMatrix.tolil())
* [ ] model.S does not support assignment (or if it does, then re-compute all stoichiometry on __setattr__)
* [ ] model.lower_bounds (etc.) update reactions/metabolites on __setitem__
* [ ] model.lower_bounds (etc.) update all reactions/metabolites on __setattr__
* [ ] unit tests
* [ ] performance assessment and optimization